RetrogeneDB ID: retro_cfam_915

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 2:5085496..5086766(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCAFG00000019817
• Aliases: None
• Description: None

Sequence

>retro_cfam_915
GCGCCCGCGGGGATCCCGGGGAACCCGCGGGAGGTCTCCAACCCCGCCAAGCCTGGCCGCAAGACCAAGCAGCTGCAGTA
CGCGCAGAACGTGGTGGTAAAGACGCCCTGGAATCACCAGCTCGCCTGGCCCTTCTACCAGCCCGTGGATGCAATCAAGC
TAACCTTGCCCGATTACCATAAAATCATAAACACCCGATGGCTATGGGGACTATTCAGAAGAGACTAGAAAATAATTATT
ACTGGAGCGCCAGCGAATGCGTGCAGGACTTCCACACCATGTTTACAAATTGTTACATTTACAACAAGCCCACAGATGAC
ACAGTGCTAACGGCCCAAGCCTTAGAGAAAATTTTTCTGCAGAGAGTGGCCCAGGTGCCCCAGGACGAAGTTGAATTATT
ACCCCCTGCTCCGAAGGGCAAAGGCCGGAACGCGGCGCAGGAACCCGGAGTGCAGGTGGGCAGCAAGTGGTGGCCGTGTC
CTCTGTCTCCCCAGCAACCCCCTTCCAGAGCGTCCCCCCACTGTCTCCAGACGCCTGTCATTGCTGCCCCCCCTCTGCCA
ACCATTACCGCAAACATCACGTCGGTCCCTGCGCCCCCGCCGCCGCCCCACCCCCTCCCTCGACGCCCATCATCCATCCC
TGTGGTCCCTCCCACAGCGCCTGTCGTCAAGGAAAAGGGTGCAAAGCGGAAAGCAGCCACCACGACGCCCACTCCATCCG
CGAGCCGGAGCGAATCGCCGCCGCCATCGTCAGACCCCAAGCAGGCCGAGGTGGGGGCTCGGCGAGAGAGTGGGGGCCGC
CCCATCGCACCGCCCTGGAAGGGTCTAGAGGACGGCGAGGTGCCTCAGCATGCGGGCCGGAAGGGCGAGCTGCCGAGCAC
TCGCGGCACTGTGACAGCGTCCTCGAGGACATGCCGTGCAAGAAGCGTGCGGCCTGCGCCTGGCCCTTCTCCAGCCGGTG
GACGCCGAGGCCCTGGAGCTGCACGACTACCACGACGTCACCGAGCACCCGATGGACCTTAGCACTGTCAAGAAGACGGA
CAGTCGCGAGTGCCCAGACGCGCAGGGCTTCGCTGCTGACACCCGGTTCATGTTCTCCAGCTGTTACCAGTACAACCCCC
AGGCCACAAGGTGGTGGCCGTGGCCAGGAAGCTGCGGCCGTGTTTGAGGTGCGGTTTGCTAAGATGCCGGCTGAGCCGGG
GGAGGCGCCGGCCCTGCCTGCGCCCGCAGCCCCCGTGCTGAGCAGGGGCGCCGAGAGCAGCCGCAGCAGC

Alignment

ORF - retro_cfam_915 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.77 %
• Parental protein coverage: 58.93 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 10

Retrocopy - Parental Gene Alignment:

Parental  APGPVNPPPPEVSNPAKPGRKTNQLQYMQNVVVKTLWKHQFAWPFYQPVDAIKLNLPDYHKII-KNPMDM
          AP......P.EVSNPAKPGRKT.QLQY.QNVVVKT.W.HQ.AWPFYQPVDAIKL.LPDYHKII.K.PM.M
Retrocopy APAGIPGNPREVSNPAKPGRKTKQLQYAQNVVVKTPWNHQLAWPFYQPVDAIKLTLPDYHKII<KHPMAM

Parental  GTIKKRLENNYYWSASECMQDFNTMFTNCYIYNKPTDDIVLMAQALEKIFLQKVAQMPQEEVELLPPAPK
          GTI.KRLENNYYWSASEC.QDF.TMFTNCYIYNKPTDD.VL.AQALEKIFLQ.VAQ.PQ.EVELLPPAPK
Retrocopy GTIQKRLENNYYWSASECVQDFHTMFTNCYIYNKPTDDTVLTAQALEKIFLQRVAQVPQDEVELLPPAPK

Parental  GKGRKPA-AGTQSAGTQQVVAVSSVSPATPFQSV-PPTVS-QTPVIAATPVPTITANITSVPVP-PAAAP
          GKGR..A.AGT.SAG.QQVVAVSSVSPATPFQSV.PPTVS.QTPVIAA.P.PTITANITSVP.P.PAAAP
Retrocopy GKGRNAA<AGTRSAGGQQVVAVSSVSPATPFQSV<PPTVS<QTPVIAAPPLPTITANITSVPAP<PAAAP

Parental  PPPSTPII-PVVP-PTPPVVKKKGVKRKADTTTPTTSAITASRSESPPPLSDPKQAKVVARRESGGRPIK
          PPPSTPII.P..P.PT.PVVK.KG.KRKA.TTTPT.SA...SRSESPPP.SDPKQA.V.ARRESGGRPI.
Retrocopy PPPSTPIIHPCGP>PTAPVVKEKGAKRKAATTTPTPSA---SRSESPPPSSDPKQAEVGARRESGGRPIA

Parental  PPKKDLEDGEVPQHAGKKGKL-SEHLRHCDSILKEMLSKKHAAYAWPF-YKPVDAEALELHDYHDIIKHP
          PP.K.LEDGEVPQHAG.KG.L..EH.RHCDS.L..M..KK.AA.AWPF...PVDAEALELHDYHD...HP
Retrocopy PPWKGLEDGEVPQHAGRKGEL<AEHSRHCDSVLEDMPCKKRAACAWPF<LQPVDAEALELHDYHDVTEHP

Parental  MDLSTVKKKMDSREYPDAQGFAADIRLMFSNCYKYN-PPDHEVVAMARKLQD-VFEMRFAKMPDEPVEAP
          MDLSTV.KK.DSRE.PDAQGFAAD.R.MFS.CY.YN.PP.H.VVA.ARKL...VFE.RFAKMP.EP.EAP
Retrocopy MDLSTV-KKTDSRECPDAQGFAADTRFMFSSCYQYN<PPGHKVVAVARKLRP<VFEVRFAKMPAEPGEAP

Parental  ALPAPAAPVLSKGAESSRSS
          ALPAPAAPVLS.GAESSRSS
Retrocopy ALPAPAAPVLSRGAESSRSS

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP012049_cerebellum	0.00 RPM	128.98 RPM
SRP017611_brain	0.00 RPM	36.68 RPM
SRP017611_kidney	0.00 RPM	34.08 RPM
SRP017611_liver	0.00 RPM	21.39 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_915 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_915 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_915 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000019817	2 retrocopies	retro_cfam_915 , retro_cfam_916,